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At least 163 records · Page 9Linked to original sources
USGS2013

Worldwide phylogenetic relationship of avian poxviruses

Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of the Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups, and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g., starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

Journal of Virology↗
USGS1993

Coupled effects of vertical mixing and benthic grazing on phytoplankton populations in shallow, turbid estuaries

Coastal ocean waters tend to have very different patterns of phytoplankton biomass variability from the open ocean, and the connections between physical variability and phytoplankton bloom dynamics are less well established for these shallow systems. Predictions of biological responses to physical variability in these environments is inherently difficult because the recurrent seasonal patterns of mixing are complicated by aperiodic fluctuations in river discharge and the high-frequency components of tidal variability. We might expect, then, less predictable and more complex bloom dynamics in these shallow coastal systems compared with the open ocean. Given this complex and dynamic physical environment, can we develop a quantitative framework to define the physical regimes necessary for bloom inception, and can we identify the important mechanisms of physical-biological coupling that lead to the initiation and termination of blooms in estuaries and shallow coastal waters? Numerical modeling provides one approach to address these questions. Here we present results of simulation experiments with a refined version of Cloern's (1991) model in which mixing processes are treated more realistically to reflect the dynamic nature of turbulence generation in estuaries. We investigated several simple models for the turbulent mixing coefficient. We found that the addition of diurnal tidal variation to Cloern's model greatly reduces biomass growth indicating that variations of mixing on the time scale of hours are crucial. Furthermore, we found that for conditions representative of South San Francisco Bay, numerical simulations only allowed for bloom development when the water column was stratified and when minimal mixing was prescribed in the upper layer. Stratification, however, itself is not sufficient to ensure that a bloom will develop: minimal wind stirring is a further prerequisite to bloom development in shallow turbid estuaries with abundant populations of benthic suspension feeders.

Journal of Marine Research↗
USGS2023

Isothermal recombinant polymerase amplification and CRIPSR (CAS12A) assay detection of Renibacterium salmoninarum as an example for wildlife pathogen detection in environmental DNA samples

Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon ( Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum , is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20–40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.

Journal of Wildlife Diseases↗
USGS1970

Comparison of chemical hydrogeology of the carbonate peninsulas of Florida and Yucatan

Aquifers of the peninsulas of Florida and northern Yucatan are Tertiary marine carbonate formations showing many lithologic and faunal similarities. In addition, the tropical to subtropical climates of the two areas are similar, each having annual rainfall of about 1000 to 1500 mm. Despite similarities in these fundamental controls, contrasts in the hydrologic and geochemical systems are numerous and striking. For example, Florida has many rivers; Yucatan has none. Maximum thickness of fresh ground water in Florida is about 700 meters; in the Yucatan it is less than 70 meters. In Florida the gradient of the potentiometric surface averages about 1 meter per kilometer; in the Yucatan it is exceedingly low, averaging about 0.02 meter per kilometer. In Florida the chemical character of water changes systematically downgradient, owing to solution of minerals of the aquifer and corresponding increases in total dissolved solids, sulfate, calcium, and Mg-Ca ratio; in the Yucatan no downgradient change exists, and dominant processes controlling the chemical character of the water are solution of minerals and simple mixing of the fresh water and the body of salt water that underlies the peninsula at shallow depth. Hydrologic and chemical differences are caused in part by the lower altitude of the Yucatan plain. More important, however, these differences are due to the lack of an upper confining bed in Yucatan that is hydrologically equivalent to the Hawthorn Formation of Florida. The Hawthorn cover prevents recharge and confines the artesian water except where it is punctured by sinkholes, but sands and other unconsolidated sediments fill sinkholes and cavities and impede circulation. In the Yucatan the permeability of the entire section is so enormous that rainfall immediately infiltrates to the water table and then moves laterally to discharge areas along the coasts.

Florida Peninsula, Yucatan Peninsula↗
USGS2017

Indicator-driven conservation planning across terrestrial, freshwater aquatic, and marine ecosystems of the south Atlantic, USA

Systematic conservation planning, a widely used approach to identify priority lands and waters, uses efficient, defensible, and transparent methods aimed at conserving biodiversity and ecological systems. Limited financial resources and competing land uses can be major impediments to conservation; therefore, participation of diverse stakeholders in the planning process is advantageous to help address broad-scale threats and challenges of the 21st century. Although a broad extent is needed to identify core areas and corridors for fish and wildlife populations, a fine-scale resolution is needed to manage for multiple, interconnected ecosystems. Here, we developed a conservation plan using a systematic approach to promote landscape-level conservation within the extent of the South Atlantic Landscape Conservation Cooperative. Our objective was to identify the highest-ranked 30% of lands and waters within the South Atlantic deemed necessary to conserve ecological and cultural integrity for the 10 primary ecosystems of the southeastern United States. These environments varied from terrestrial, freshwater aquatic, and marine. The planning process was driven by indicators of ecosystem integrity at a 4-ha resolution. We used the program Zonation and 28 indicators to optimize the identification of lands and waters to meet the stated objective. A novel part of our study was the prioritization of multiple ecosystems, and we discuss the advantages and disadvantages of this approach. The evaluation of indicator representation within prioritizations was a useful method to show where improvements could be made; some indicators dictated hotspots, some had a limited extent and were well represented, and others had a limited effect. Overall, we demonstrate that a broad-scale (408,276 km 2 of terrestrial and 411,239 km 2 of marine environments) conservation plan can be realized at a fine-scale resolution, which will allow implementation of the regional plan at a local level relevant to decision making.

Journal of Fish and Wildlife Management↗
USGS2000

Responses of stable bay-margin and barrier-island systems to Holocene sea-level highstands, western Gulf of Mexico

The microtidal, wave-dominated coast of the western Gulf of Mexico displays a variety of Holocene geomorphic features indicating higher-than-present water levels that were previously attributed to storm processes while geoidal sea level was at its present position. Field and aerial-photograph examinations of bay margins, barrier islands, and beach-ridge plains following major hurricanes show that the elevated features are inundated periodically by high storm surge. Despite their inundation, these highstand features are not modified by modern storm processes. Instead, storm-related erosion and deposition are always seaward of and lower than the highstand features and are always limited to the extant shorezone, where elevations typically are less than 1.5 m above present sea level. Bay-margin and lagoonal highstand indicators include raised marshes and subtidal flats, wave-cut benches, abandoned wave-cut scarps with fringing marshes and/or beach ridges, and accretionary islands and recurved spits. Other emergent marine features include abandoned compound flood-tidal delta and washover fan complexes attached to barrier islands and anomalously high beach ridges within both the barrier-island complexes and beach-ridge plains. The highest beach ridges, raised marshes and flats, and erosional scarps and benches are manifestations of one or more rising phases and highstands in sea level, whereas the lower marshes and accretionary topography are mainly products of the falling phases and shoreface adjustment to present sea level. Different elevations of beach-ridge sets, discordant truncation of beach ridges, and elevated marine- and brackish-water faunal assemblages preserved in beach ridges, raised marshes and flats, and natural levees are compelling evidence of sea-level fluctuations of ±1 to 1.5 m from about 5500 to 1200 cal yr BP. Independent evidence from studies of geodynamic, climatic, and glacio-eustatic processes can explain the mid-Holocene highstands and late Holocene lowering of sea level that is observed in tectonically stable coastal regions far from former centers of glaciation.

Journal of Sedimentary Research↗
USGS2007

Smallmouth bass and largemouth bass predation on juvenile Chinook salmon and other salmonids in the Lake Washington basin

We assessed the impact of predation by smallmouth bass Micropterus dolomieu and largemouth bass M. salmoides on juveniles of federally listed Chinook salmon Oncorhynchus tshawytscha and other anadromous salmonid populations in the Lake Washington system. Bass were collected with boat electrofishing equipment in the south end of Lake Washington (February-June) and the Lake Washington Ship Canal (LWSC; April-July), a narrow waterway that smolts must migrate through to reach the marine environment. Genetic analysis was used to identify ingested salmonids to obtain a more precise species-specific consumption estimate. Overall, we examined the stomachs of 783 smallmouth bass and 310 largemouth bass greater than 100 mm fork length (FL). Rates of predation on salmonids in the south end of Lake Washington were generally low for both black bass species. In the LWSC, juvenile salmonids made up a substantial part of bass diets; consumption of salmonids was lower for largemouth bass than for smallmouth bass. Smallmouth bass predation on juvenile salmonids was greatest in June, when salmonids made up approximately 50% of their diet. In the LWSC, overall black bass consumption of salmonids was approximately 36,000 (bioenergetics model) to 46,000 (meal turnover consumption model) juveniles, of which about one-third was juvenile Chinook salmon, one-third was coho salmon O. kisutch, and one-third was sockeye salmon O. nerka. We estimated that about 2,460,000 juvenile Chinook salmon (hatchery and wild sources combined) were produced in the Lake Washington basin in 1999; thus, the mortality estimates in the LWSC range from 0.5% (bioenergetics) to 0.6% (meal turnover). Black bass prey mostly on subyearlings of each salmonid species. The vulnerability of subyearlings to predation can be attributed to their relatively small size; their tendency to migrate when water temperatures exceed 15??C, coinciding with greater black bass activity; and their use of nearshore areas, where overlap with black bass is greatest. We conclude that under current conditions, predation by smallmouth bass and largemouth bass has a minor impact on Chinook salmon and other salmonid populations in the Lake Washington system. ?? Copyright by the American Fisheries Society 2007.

North American Journal of Fisheries Management↗
USGS2021

Mapping biological soil crusts in a Hawaiian dryland

Historical and ongoing land use patterns in the Hawaiian Islands have degraded the Islands’ drylands, causing erosion and detrimentally affecting adjacent coastal marine ecosystems. Biological soil crust (biocrust) communities have been shown to increase soil stability in drylands worldwide, but their efficacy in mitigating soil erosion in Hawaiian drylands is largely unknown. Using a combination of field data and imagery collected by small unmanned aerial systems (sUAS), we mapped biocrusts and examined their influence on soil stability in the Kawaihae watershed, an erosion-prone dryland on leeward Hawai`i Island. We created classified maps of biocrust cover from imagery collected at three spatial resolutions (1.2, 2.1 and 2.8 cm/pixel) using the pixel-based Support Vector Machine (SVM) classifier and investigated the impacts of spatial resolution and biocrust level of development on classification accuracy. Our medium (2.1 cm) resolution image produced the highest overall classification accuracy when biocrust was treated as a single class (82.1%). We explored the spatial impacts of biocrusts on soil loss via sUAS-derived measurements of elevation change over a four-year time span. We found differences in soil loss among land cover types, but robustly quantifying these was a challenge, as much of the change fell below statistically significant limits of detection. We investigated the relationship between biocrust development and soil stability by conducting soil aggregate stability testing at the three biocrust levels of development (LODs) present at the study site. We found a significant increase in soil stability from soils without surface biocrusts (LOD score of 0) to those with biocrusts at any development level (LOD 1–3). Our research adds to the body of biocrust knowledge by presenting new information about biocrust distribution and soil stabilization capabilities in Hawaiian drylands. We also provide insights into the trade-offs between spatial resolution and classification accuracy for biocrust classification and land cover analysis.

Hawaii↗
USGS2025

Multiscale framework for assessing land cover change on barrier islands from extreme storms and restoration

Often found along the estuarine-marine interface, barrier islands and mainland coastal zones are shaped by tides, currents, extreme storms, and relative sea-level rise. These systems provide ecosystem services such as storm surge and wave attenuation, erosion protection to inland areas, habitat for fish and wildlife, recreation, and tourism. Given the importance of these ecosystems coupled with their dynamic nature, information on how these coastal systems are changing can help to inform natural resource management. Remote sensing advancements have led to an abundance of data for monitoring change in coastal settings. This study developed a multiscale framework that can provide trajectory information from screening-level analyses by using existing or custom moderate spatial resolution land cover maps. Using the north-central Gulf Coast as a case study, the trajectory of land cover area for barrier islands and mainland coastal zones was assessed using several geospatial data sets, including: (1) long-term moderate-resolution remote sensing products with an annual (or more frequent) temporal frequency; (2) a restoration database ( e.g. , beach/dune restoration, sediment placement, and dune enhancement); and (3) a tropical storm database. Due to the coarser spatial resolution of data sets used for screening-level analyses, detailed or application-specific analyses are often needed to reduce uncertainty in smaller changes that may not be captured. These may include land cover change analyses ( i.e. this study), periodic land cover maps with higher spatial resolution and more detailed land cover classes, or elevation-related analyses ( e.g. , dune change or inundation change). Using this framework, abrupt changes in land cover on Dauphin Island, Alabama, resulting from extreme storms were detected using moderate spatial resolution screening-level data, while restoration impact analyses may require higher resolution data. Further, land cover change analyses that incorporate change allocation provide robust information for understanding land cover change in dynamic coastal settings.

Alabama, Florida↗
USGS2022

Diatom influence on the production characteristics of hydrate-bearing sediments: Examples from Ulleung Basin, offshore South Korea

The Ulleung Basin Gas Hydrate field expeditions in 2007 (UBGH1) and 2010 (UBGH2) sought to assess the Basin's gas hydrate resource potential. Coring operations in both expeditions recovered evidence of gas hydrate, primarily as fracture-filling (or vein type) morphologies in mainly silt-sized, fine-grained sediment, but also as pore-occupying hydrate in the coarser-grained layers of interbedded sand and fine-grained systems. A commonality across many of these occurrences is the presence of diatoms in the fine-grained sediment. Here we tested fine-grained sediment (median grain size <12.5 μm) associated with hydrate occurrences at four UBGH2 sites (UBGH2-2-2, UBGH2-3, UBGH2-6 and UBGH2-11) to investigate potential impacts of diatoms on efforts to extract methane from hydrate, or to tap hydrocarbon reservoirs beneath hydrate-bearing sediment. Two key considerations are: the extent to which diatoms control sediment mechanical properties, and the extent to which pore-water freshening, which occurs as gas hydrate breaks down during resource extraction, alters the diatom control on sediment mechanical properties. We conducted experiments to measure sediment index properties, sedimentation behavior and compressibility to address these considerations. We relied on scanning electron microscope (SEM) imagery and X-ray powder diffraction (XRD) to characterize the sediment mineralogy. Our high-level findings are that at the ∼20–45% (by volume) diatom concentrations observed at these UBGH2 sites, sediment compressibility increases with diatom content, but diatoms only appear to increase porosity and permeability at the highest diatom concentration (∼45%). Our measurements suggest in situ compression indices of 0.35–0.55 and permeabilities on the order of 0.01milliDarcies (1 × 10 −17 m 2 ) can be anticipated at these sites. Importantly, these properties are not expected to vary significantly upon pore water freshening that accompanies gas hydrate dissociation during production.

East Sea, Ulleung Basin↗
USGS2020

Oil-source rock correlation studies in the unconventional Upper Cretaceous Tuscaloosa marine shale (TMS) petroleum system, Mississippi and Louisiana, USA

The U.S. Geological Survey assessed undiscovered unconventional hydrocarbon resources reservoired in the Upper Cretaceous Tuscaloosa marine shale (TMS) of southern Mississippi and adjacent Louisiana in 2018. As part of the assessment, oil-source rock correlations were examined in the TMS play area where operators produce light (38–45° API), sweet oil from horizontal, hydraulically-fractured wells in an overpressured ‘high-resistivity’ (>5 Ω-m) zone at the base of the TMS. Geochemical data from 39 oil samples and 17 source rock solvent extracts collected from the TMS play area indicate close correspondence for Tuscaloosa Group oils [from lower Tuscaloosa, middle Tuscaloosa (the TMS) and upper Tuscaloosa reservoirs] in thermal maturity (computed from MPI), SARA proportions, n- alkane distributions, isoprenoid and DBT/P ratios, monoaromatic steroids, and δ 13 C isotopic compositions (from whole oils, saturate and aromatic fractions). Other parameters (normal steranes, extended homohopanes, C 31 R/C 30 hopane, norhopane/hopane and tricyclic terpane ratios, gammacerane/hopane) show most oil samples have similar values, suggesting all Tuscaloosa Group oils are from a common mixed marine-terrigenous source rock. Tighter distributions for triaromatic steroid (TAS) and δ 13 C isotopic composition for conventional oils in lower and upper Tuscaloosa reservoirs may indicate charge occurred in a single or shorter pulse relative to TMS oils which show broader TAS and δ 13 C properties, possibly from their generation over an extended period of burial maturation. Dissimilarity in geochemical properties between lower Tuscaloosa source rock solvent extracts and Tuscaloosa Group oils indicates lower Tuscaloosa source rocks did not contribute significantly to conventional and unconventional Tuscaloosa Group hydrocarbon accumulations. Whereas, TMS solvent extracts are similar to Tuscaloosa Group oils, suggesting an oil-source rock correlation. Excluding the possibility for long-distance lateral migration from a similar source downdip (which is unnecessary given thermal maturity considerations), the observations indicate 1. the TMS is a self-sourced reservoir, 2. the TMS is the source of oils accumulated in nearby conventional Tuscaloosa Group reservoirs, and 3. thin organic-rich shales in the lower Tuscaloosa did not contribute substantially to any oil accumulations in the Tuscaloosa Group.

Louisiana, Mississippi↗
USGS2010

EAARL coastal topography-western Florida, post-Hurricane Charley, 2004: seamless (bare earth and submerged.

Project Description These remotely sensed, geographically referenced elevation measurements of lidar-derived seamless (bare-earth and submerged) topography were produced as a collaborative effort between the U.S. Geological Survey (USGS), Coastal and Marine Geology Program (CMGP), St. Petersburg, FL, and the National Aeronautics and Space Administration (NASA), Wallops Flight Facility, VA. This project provides highly detailed and accurate datasets of a portion of the western Florida coastline beachface, acquired post-Hurricane Charley on August 17 and 18, 2004. The datasets are made available for use as a management tool to research scientists and natural-resource managers. An innovative airborne lidar instrument originally developed at the NASA Wallops Flight Facility, and known as the Experimental Advanced Airborne Research Lidar (EAARL), was used during data acquisition. The EAARL system is a raster-scanning, waveform-resolving, green-wavelength (532-nanometer) lidar designed to map near-shore bathymetry, topography, and vegetation structure simultaneously. The EAARL sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive lidar, a down-looking red-green-blue (RGB) digital camera, a high-resolution multispectral color infrared (CIR) camera, two precision dual-frequency kinematic carrier-phase GPS receivers, and an integrated miniature digital inertial measurement unit, which provide for sub-meter georeferencing of each laser sample. The nominal EAARL platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL system, and the resulting data were then processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of lidar data in an interactive or batch mode. Modules for presurvey flight-line definition, flight-path plotting, lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is used routinely to create maps that represent submerged or sub-aerial topography. Specialized filtering algorithms have been implemented to determine the 'bare earth' under vegetation. For more information about similar projects, please visit the Decision Support for Coastal Science and Management website. Selected References Brock, J.C., Wright, C.W., Sallenger, A.H., Krabill, W.B., and Swift, R.N., 2002, Basis and methods of NASA airborne topographic mapper Lidar surveys for coastal studies: Journal of Coastal Research, v. 18, no. 1, p. 1-13. Crane, Michael, Clayton, Tonya, Raabe, Ellen, Stoker, Jason, Handley, Larry, Bawden, Gerald, Morgan, Karen, and Queija, Vivian, 2004, Report of the U.S. Geological Survey Lidar workshop sponsored by the Land Remote Sensing Program and held in St. Petersburg, FL, November 2002: U.S. Geological Survey Open-File Report 2004-1456, 72 p. Nayegandhi, Amar, Brock, J.C., and Wright, C.W., 2009, Small-footprint, waveform-resolving Lidar estimation of submerged and sub-canopy topography in coastal environments: International Journal of Remote Sensing, v. 30, no. 4, p. 861-878. Sallenger, A.H., Wright, C.W., and Lillycrop, Jeff, 2005, Coastal impacts of the 2004 hurricanes measured with airborne Lidar; initial results: Shore and Beach, v. 73, nos. 2-3, p. 10-14. Resources Included Readme.txt File

Data Series↗
USGS1995

Seafloor environments within the Boston Harbor- Massachusetts Bay sedimentary system: A regional synthesis

Modern seafloor sedimentary environments within the glaciated, topographically complex Boston Harbor and Massachusetts Bay area have been interpreted and mapped from an extensive collection of sidescan sonar records and supplemental marine geologic data. Three categories of environments are present that reflect the dominant long-term processes of erosion or nondeposition, deposition, and sediment reworking. (1) Environments of erosion or nondeposition comprise exposures of bedrock, glacial drift, coarse lag deposits, and possibly coastal plain rocks that contain sediments (where present) ranging from boulder fields to gravelly sands and occur in areas of relatively strong currents. (2) Environments of deposition contain fine-grained sediments ranging from muddy sands to muds that have accumulated in areas of predominantly weak bottom currents. (3) Environments of sediment reworking contain patches with textures ranging from sandy gravels to muds that have been produced by a combination of erosion and deposition in areas with variable bottom currents. The distribution of sedimentary environments across the Boston Harbor-Massachusetts Bay area is extremely patchy. Locally, this patchiness is due either to modifications of bottom-current strength (caused by the irregular topography and differences in water depth) or to small-scale changes in the supply of fine-grained sediments. Regional patchiness, however, reflects differences in geologic and oceanographic conditions among the estuarine, inner shelf, and basinal parts of the sedimentary system. The estuarine part of the system (Boston Harbor) is a depositional trap for fine-grained sediments because it is protected from large waves, has generally weak and variable tidal currents, and receives a large supply of fine grained detritus from natural and anthropogenic sources. The inner shelf, on the other hand, is largely an area of erosion or nondeposition due to sediment removal and redistribution during past sea-level changes, to sediment resuspension and winnowing by modern waves and currents, and to an inadequate supply of fine-grained sediments. The basinal part of the system (Stellwagen Basin) is mainly a tranquil depositional environment in which fine-grained sediments from several potential sources settle through the water column and accumulate under weak bottom currents. This study indicates areas within the Boston Harbor-Massachusetts Bay sedimentary system where fine-grained sediments and associated contaminants are likely to be either moved or deposited. It also provides a guide to the locations and variability of benthic habitats.

Massachusetts Bay↗
USGS1989

Characterization of coal-derived hydrocarbons and source-rock potential of coal beds, San Juan Basin, New Mexico and Colorado, U.S.A.

Coal beds are considered to be a major source of nonassociated gas in the Rocky Mountain basins of the United States. In the San Juan basin of northwestern New Mexico and southwestern Colorado, significant quantities of natural gas are being produced from coal beds of the Upper Cretaceous Fruitland Formation and from adjacent sandstone reservoirs. Analysis of gas samples from the various gas-producing intervals provided a means of determining their origin and of evaluating coal beds as source rocks. The rank of coal beds in the Fruitland Formation in the central part of the San Juan basin, where major gas production occurs, increases to the northeast and ranges from high-volatile B bituminous coal to medium-volatile bituminous coal ( R m values range from 0.70 to 1.45%). On the basis of chemical, isotopic and coal-rank data, the gases are interpreted to be thermogenic. Gases from the coal beds show little isotopic variation ( δ 13 C 1 values range −43.6 to −40.5 ppt), are chemically dry (C 1 /C 1–5 values are > 0.99), and contain significant amounts of CO 2 (as much as 6%). These gases are interpreted to have resulted from devolatilization of the humic-type bituminous coal that is composed mainly of vitrinite. The primary products of this process are CH 4 , CO 2 and H 2 O. The coal-generated, methane-rich gas is usually contained in the coal beds of the Fruitland Formation, and has not been expelled and has not migrated into the adjacent sandstone reservoirs. In addition, the coal-bed reservoirs produce a distinctive bicarbonate-type connate water and have higher reservoir pressures than adjacent sandstones. The combination of these factors indicates that coal beds are a closed reservoir system created by the gases, waters, and associated pressures in the micropore coal structure. In contrast, gases produced from overlying sandstones in the Fruitland Formation and underlying Pictured Cliffs Sandstone have a wider range of isotopic values ( δ 13 C 1 values range from −43.5 to −38.5 ppt), are chemically wetter (C 1 /C 1–5 values range from 0.85 to 0.95), and contain less CO 2 (< 2%). These gases are interpreted to have been derived from type III kerogen dispersed in marine shales of the underlying Lewis Shale and nonmarine shales of the Fruitland Formation. In the underlying Upper Cretaceous Dakota Sandstone and Tocito Sandstone Lentil of the Mancos Shale, another gas type is produced. This gas is associated with oil at intermediate stages of thermal maturity and is isotopically lighter and chemically wetter at the intermediate stage of thermal maturity as compared with gases derived from dispersed type III kerogen and coal; this gas type is interpreted to have been generated from type II kerogen. Organic matter contained in coal beds and carbonaceous shales of the Fruitland Formation has hydrogen indexes from Rock-Eval pyrolysis between 100 and 350, and atomic H:C ratios between 0.8 and 1.2. Oxygen indexes and atomic O:C values are less than 24 and 0.3, respectively. Extractable hydrocarbon yields are as high as 7,000 ppm. These values indicate that the coal beds and carbonaceous shales have good potential for the generation of liquid hydrocarbons. Voids in the coal filled with a fluorescent material that is probably bitumen is evidence that liquid hydrocarbon generation has taken place. Preliminary oil-source rock correlations based on gas chromatography and stable carbon isotope ratios of C 15+ hydrocarbons indicate that the coals and (or) carbonaceous shales in the Fruitland Formation may be the source of minor amounts of condensate produced from the coal beds at relatively low levelsof thermal maturity ( R m =0.7).

International Journal of Coal Geology↗
USGS2008

Progression in sulfur isotopic compositions from coal to fly ash: Examples from single-source combustion in Indiana

Sulfur occurs in multiple mineral forms in coals, and its fate in coal combustion is still not well understood. The sulfur isotopic composition of coal from two coal mines in Indiana and fly ash from two power plants that use these coals were studied using geological and geochemical methods. The two coal beds are Middle Pennsylvanian in age; one seam is the low-sulfur (< 1%) Danville Coal Member of the Dugger Formation and the other is the high-sulfur (> 5%) Springfield Coal Member of the Petersburg Formation. Both seams have ash contents of approximately 11%. Fly-ash samples were collected at various points in the ash-collection system in the two plants. The results show notable difference in ??34S for sulfur species within and between the low-sulfur and high-sulfur coal. The ??34S values for all sulfur species are exclusively positive in the low-sulfur Danville coal, whereas the ??34S values for sulfate, pyritic, and organic sulfur are both positive and negative in the high-sulfur Springfield coal. Each coal exhibits a distinct pattern of stratigraphic variation in sulfur isotopic composition. Overall, the ??34S for sulfur species values increase up the section in the low-sulfur Danville coal, whereas they show a decrease up the vertical section in the high-sulfur Springfield coal. Based on the evolution of ??34S for sulfur species, it is suggested that there was influence of seawater on peat swamp, with two marine incursions occurring during peat accumulation of the high-sulfur Springfield coal. Therefore, bacterial sulfate reduction played a key role in converting sulfate into hydrogen sulfide, sulfide minerals, and elemental sulfur. The differences in ??34S between sulfate sulfur and pyritic sulfur is very small between individual benches of both coals, implying that some oxidation occurred during deposition or postdeposition. The ??34S values for fly ash from the high-sulfur Springfield coal (averaging 9.7???) are greatly enriched in 34S relative to those in the parent coal (averaging 2.2???). This indicates a fractionation of sulfur isotopes during high-sulfur coal combustion. By contrast, the ??34S values for fly-ash samples from the low-sulfur Danville coal average 10.2???, only slightly enriched in 34S relative to those from the parent coal (average 7.5???). The ??34S values for bulk S determined directly from the fly-ash samples show close correspondence with the ??34S values for SO4- 2 leached from the fly ash in the low-sulfur coal, suggesting that the transition from pyrite to sulfate occurred via high-temperature oxidation during coal combustion. ?? 2007 Elsevier B.V. All rights reserved.

International Journal of Coal Geology↗
USGS2026

An integrated mudstone facies classification scheme and revised interpretation of the sedimentologic processes driving carbon burial in the Cenomanian–Turonian Greenhorn Formation, Colorado, U.S.A.

Standardizing facies descriptions has proven key to integrating interpretations of depositional processes and environments from sedimentologic observations with geochemistry data for mudstone lithologies. Because of their fine-grained nature, high degree of compaction, and heterogeneous composition, standardizing methods for mudstone descriptions has proven difficult, but it is critical to formulating meaningful interpretations of the processes that govern the accumulation of organic-rich lithologies and their role in both petroleum systems and the global carbon cycle. In this study, we have developed a modified facies classification scheme for mudstone lithologies that incorporates sedimentologic and compositional observation at the hand-sample and thin-section scales with geochemical measurements, including bulk organic and inorganic geochemistry, to characterize these rocks and their variability more completely for improved interpretations of depositional environments during a low-order sea-level transgression. The facies described in this study are of the Cenomanian–Turonian Greenhorn Formation in the USGS #1 Portland Core drilled in Fremont County, Colorado. Strata of the Greenhorn Formation span Oceanic Anoxic Event 2 (OAE-2) and the preceding interval. Lithologies range from organic-rich argillaceous mudstones with varied sedimentary structures to organic-lean, highly bioturbated limestones. Six facies were identified, each differentiated by varied sedimentary structures and geochemical composition. These facies occur in a predictable stratigraphic stacking pattern that represents a low-order sea-level transgression with interpreted depositional environments ranging from terrigenous-dominated pro-delta and muddy continental shelf at the base of the interval to pelagic offshore marine at the top of the Greenhorn Formation. Though the facies are consistent with previous interpretations of depositional environments at this locale in the Cretaceous Western Interior Seaway during the Greenhorn cyclothem, the sedimentary processes governing the accumulation of organic-rich strata that have defined this interval are significantly revised. Variability in the proximity and intensity of bottom currents driven by storms and geostrophic flows were key to the accumulation of each facies, with significant sediment transport occurring even through deposition in the most oxygen-depleted bottom waters. The methodology and interpretations provided here are now being employed to basin-scale predictions of organic enrichment utilizing calibrated petrophysical methods. The approach and results from this study improve understanding of how organic and inorganic carbon was sequestered during perturbations to the global carbon cycle associated with events such as OAE-2.

Colorado↗
USGS2013

Evaluating a multispecies adaptive management framework: Must uncertainty impede effective decision-making?

Application of adaptive management to complex natural resource systems requires careful evaluation to ensure that the process leads to improved decision-making. As part of that evaluation, adaptive policies can be compared with alternative nonadaptive management scenarios. Also, the value of reducing structural (ecological) uncertainty to achieving management objectives can be quantified. A multispecies adaptive management framework was recently adopted by the Atlantic States Marine Fisheries Commission for sustainable harvest of Delaware Bay horseshoe crabs Limulus polyphemus, while maintaining adequate stopover habitat for migrating red knots Calidris canutus rufa , the focal shorebird species. The predictive model set encompassed the structural uncertainty in the relationships between horseshoe crab spawning, red knot weight gain and red knot vital rates. Stochastic dynamic programming was used to generate a state-dependent strategy for harvest decisions given that uncertainty. In this paper, we employed a management strategy evaluation approach to evaluate the performance of this adaptive management framework. Active adaptive management was used by including model weights as state variables in the optimization and reducing structural uncertainty by model weight updating. We found that the value of information for reducing structural uncertainty is expected to be low, because the uncertainty does not appear to impede effective management. Harvest policy responded to abundance levels of both species regardless of uncertainty in the specific relationship that generated those abundances. Thus, the expected horseshoe crab harvest and red knot abundance were similar when the population generating model was uncertain or known, and harvest policy was robust to structural uncertainty as specified. Synthesis and applications . The combination of management strategy evaluation with state-dependent strategies from stochastic dynamic programming was an informative approach to evaluate adaptive management performance and value of learning. Although natural resource decisions are characterized by uncertainty, not all uncertainty will cause decisions to be altered substantially, as we found in this case. It is important to incorporate uncertainty into the decision framing and evaluate the effect of reducing that uncertainty on achieving the desired outcomes

Journal of Applied Ecology↗
USGS2025

Evaluation of solid bitumen created from marine oil shale bituminite under hydrous and anhydrous pyrolysis conditions

To test the influence of environmental conditions on aromaticity of solid bitumen generated during petroleum generation, four organic-rich (26–36 wt% total organic carbon) oil shale samples collected from the Neoproterozoic–Lower Cambrian restricted marine Salt Range Formation in the upper Indus Basin, Pakistan, were pyrolyzed under hydrous and anhydrous conditions. Experiments used closed system batch reactors at subcritical water temperatures between 300 and 370°C for 72 h. Thermal conversion of bituminite in the Salt Range oil shales created a newly formed solid bitumen, similar to previous observations from experiments on the Eocene lacustrine Green River Formation Mahogany zone oil shale. Newly formed solid bitumen in the Salt Range Formation oil shales generally has higher reflectance (R o ) in hydrous residues compared to anhydrous experiments subjected to the same time-temperature conditions, also similar to prior observations. This finding supports the hypothesis that radical disproportionation is favored in the presence of hydrogen contributed by water, promoting aromatization in the solid bitumen residue with concomitant increased expulsion of saturated hydrocarbons. Indigenous solid bitumen (and vitrinite in a comparison sample) also shows higher reflectance values in hydrous versus anhydrous residues, indicating that additional aromatization in the presence of exogenous hydrogen occurs both in newly formed organic matter and in organic matter that is present throughout the experiment. Despite similarities in their bulk rock geochemical screening parameters, R o evolution shows different trajectories amongst the four Salt Range oil shales, suggesting as-yet undetermined differences in kinetic properties which are probably related to differences in a priori chemical composition. These results have implications for the use of solid bitumen reflectance (BR o ) as a thermal proxy, suggesting BR o values and appearance could vary as a function of the concentration of water. Variation in water concentration may be present at the reservoir or formation scale, but may also be present at a much finer scale in tight oil shales where permeability is several orders of magnitude lower than conventional reservoirs. Therefore, local variations in the presence of water potentially could explain substantial variation in BR o values and appearance in closely spaced source rock samples and even within an individual microscope field.

Journal of Analytical and Applied Pyrolysis↗